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Achalasia can happen for different reasons. It can be difficult for your doctor to find a specific cause. This condition may be hereditary, or it may be the result of an autoimmune condition. With this type of condition, your body’s immune system mistakenly attacks healthy cells in your body.
The degeneration of nerves in your esophagus often contributes to the advanced symptoms of achalasia.
Source: http://www.healthline.com/health/achalasia#causes2